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Fig. 5 | Genome Biology

Fig. 5

From: Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders

Fig. 5

TOP2B, CTCF, and RAD21 binding is spatially organized. a Distribution of TOP2B, CTCF, and RAD21 ChIP-seq peak summits relative to the center of the CTCF core motif (black arrow). Distributions before (left) and after (right) ordering the CTCF peaks according to the orientation of the CTCF motif are shown and are significantly different (p value <10–16). b Number of triple sites with different TOP2B/CTCF/RAD21 binding orders relative to the center of the CTCF motif. Counts are shown before and after accounting for the CTCF motif orientation. c Genome browser tracks showing the ChIP-seq signal of TOP2B, CTCF, and RAD21 in two example regions on chromosomes 16 and 3. The top track shows the location of CTCF core motif, with the direction of it indicated by white arrows. Black bars above ChIP-seq signal tracks indicate peak locations with the yellow lines showing the location of peak summits. d Overview of ChIP-exo. After chromatin immunoprecipitation of cross-linked and sonicated chromatin, lambda exonuclease treatment selectively digests the 5′-phosphorylated strand of dsDNA. The resulting digestion leaves strand-specific footprints of the bound protein (labeled TF in the cartoon). DNA sequencing of these ChIP-exo fragments can reveal the border of where the DNA was protected by the bound protein. ChIP-exo results can be visualized by counting the pile-ups of the 5′ ends of DNA sequence reads (we have labeled the forward strand blue and the reverse strand red). e ChIP-exo protection signal profiles for CTCF, RAD21, and TOP2B ChIP-exo and DNase-seq (DGF) experiments. Average numbers of 5′ nucleotides of ChIP-exo reads (blue: forward strand; red: reverse strand) are plotted separately for triple, double, and singleton CTCF sites at each base pair (+/– 50 bp) relative to the center of the CTCF core motif. The number of regions used to generate each plot is labeled in the top right corner. The relative position of the CTCF core motif is shown

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